The energy and its first and second geometrical derivatives obtained by Quantum Mechanical (QM) calculations for a number of conformations of a single molecule in its ground- or excited state are used to specifically parameterize the intramolecular term of a QM derived force-field (QMD-FF),[1,2,3,4] suitable for computer simulations based on classical physics as Monte Carlo (MC) or Molecular Dynamics (MD). [5,6]
As most general-purpose Force Fields (FFs),[7,8,9,10,11] a QMD-FF is built up by essentially three ingredients, namely:
- i) A set of selected generalized (or redundant) internal coordinates (RICs), such as bond lengths, angles, dihedrals, or nonbonded distances, that completely define the molecular geometry.
- ii) A set of model potential functions associated
with each RIC.
- iii) A set of parameters (force constants and RIC's equilibrium values) which complete the definition of the model functions, settling molecular chemical specificity onto the FF functional.
The JOYCE program[12] reads a starting topology file in which all selected RICs and the associated model functions that define the intramolecular potential are specified.
This file can be automatically generated by the JOYCE code (see for instance Section 3.4), created by the user through the scripts distributed at the JOYCE website,[13] or built using popular webservers. [14,15,16,17]
The supported format for this input topology file is the same as used in the GROMACS [18] package, usually referenced as .top (see Section 5.3 for further details).
The third ingredient, which consists in the final QMD-FF parameters, is created from the database purposely calculated at the QM level, specifically for the chosen molecular target molecule T.
As discussed in more detail in Sections 3.3 and 5.2, such a QM database is read by JOYCE from external files, which contain the calculated QM data.
The supported formats are: i) a formatted
3(.fcc) file, compatible, with the
3 code [19], and ii) a formatted checkpoint file (.fchk) produced by the GAUSSIAN16 package [20] (and previous releases).
All QMD-FF parameters are obtained from the data retrieved from this QM database calculated at first principle level. That is, the FF equilibrium values of all selected RICs are automatically extracted by JOYCE from the optimized QM geometry, while the force constants are calculated through a linear fitting procedure,[1,21] as detailed in Section 7.
The JOYCE code[12] is developed by Giacomo Prampolini, 1 Javier Cerezo, 2 Samuele Giannini, 3 Ivo Cacelli and Nicola De Mitri.
The current version of the code is available within the JOYCE3.0 package, maintained and distributed at the JOYCE website[13] by Pablo M. Martinez, Anna Piras, Javier Cerezo, José Pablo Galvez, Samuele Giannini, Alessandro Landi, Daniele Padula, Abderrahmane Semmeq, J. Guillherme Vilhena and Giacomo Prampolini.
The whole package is open-software: it can be redistributed and/or modified under the terms of the GNU General Public License as published by the Free Software Foundation (version 3).
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program.
If not, see http://www.gnu.org/licenses/.
For further information type, once installed:
go.joyce -lic
Please visit the JOYCE3.0 website[13] for further tutorials, templates, and downloads.